Starting phenix.real_space_refine on Fri Sep 11 22:18:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wiv_21685/09_2026/6wiv_21685.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wiv_21685/09_2026/6wiv_21685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wiv_21685/09_2026/6wiv_21685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wiv_21685/09_2026/6wiv_21685.map" model { file = "/net/cci-nas-00/data/ceres_data/6wiv_21685/09_2026/6wiv_21685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wiv_21685/09_2026/6wiv_21685.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wiv_21685/09_2026/6wiv_21685.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wiv_21685/09_2026/6wiv_21685.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 2 5.49 5 S 61 5.16 5 C 7361 2.51 5 N 1791 2.21 5 O 1990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5427 Classifications: {'peptide': 681} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 652} Chain breaks: 2 Chain: "B" Number of atoms: 5333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5333 Classifications: {'peptide': 671} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 643} Chain breaks: 3 Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 208 Unusual residues: {' CA': 1, 'CLR': 4, 'NAG': 3, 'U3G': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'CLR': 6, 'NAG': 1, 'U3D': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.45, per 1000 atoms: 0.22 Number of scatterers: 11206 At special positions: 0 Unit cell: (86.9, 97.9, 162.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 61 16.00 P 2 15.00 O 1990 8.00 N 1791 7.00 C 7361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 365 " " NAG A 902 " - " ASN A 385 " " NAG A 903 " - " ASN A 397 " " NAG B 901 " - " ASN B 404 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 561.8 milliseconds 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 58.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 67 through 85 Proline residue: A 73 - end of helix removed outlier: 3.812A pdb=" N GLU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 4.292A pdb=" N LYS A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 111 " --> pdb=" O GLN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.661A pdb=" N ASN A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 175 through 188 removed outlier: 4.127A pdb=" N THR A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 216 removed outlier: 3.722A pdb=" N GLU A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 250 through 265 removed outlier: 3.555A pdb=" N LYS A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.590A pdb=" N GLU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 349 through 368 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.571A pdb=" N ASP A 380 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 381 " --> pdb=" O LEU A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 471 through 499 removed outlier: 3.654A pdb=" N PHE A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.640A pdb=" N SER A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 526 Processing helix chain 'A' and resid 526 through 532 removed outlier: 3.509A pdb=" N LEU A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 576 removed outlier: 8.866A pdb=" N ARG A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ASN A 540 " --> pdb=" O HIS A 536 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN A 541 " --> pdb=" O ILE A 537 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) Proline residue: A 543 - end of helix removed outlier: 3.967A pdb=" N MET A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 615 removed outlier: 3.676A pdb=" N LEU A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 674 removed outlier: 3.603A pdb=" N ILE A 655 " --> pdb=" O THR A 651 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 656 " --> pdb=" O TRP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 709 removed outlier: 3.732A pdb=" N TYR A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN A 694 " --> pdb=" O MET A 690 " (cutoff:3.500A) Proline residue: A 704 - end of helix removed outlier: 3.918A pdb=" N MET A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 747 Proline residue: A 738 - end of helix Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.618A pdb=" N GLY B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 109 through 124 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.647A pdb=" N SER B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.574A pdb=" N LEU B 163 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.863A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.940A pdb=" N VAL B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 246 removed outlier: 3.698A pdb=" N ASN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 270 removed outlier: 3.760A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 removed outlier: 3.566A pdb=" N GLU B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 Processing helix chain 'B' and resid 354 through 376 removed outlier: 3.720A pdb=" N GLY B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 405 removed outlier: 3.815A pdb=" N GLY B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 506 Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.956A pdb=" N SER B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 537 Processing helix chain 'B' and resid 545 through 584 removed outlier: 3.516A pdb=" N ALA B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 619 removed outlier: 3.577A pdb=" N ASP B 619 " --> pdb=" O TRP B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 679 removed outlier: 3.594A pdb=" N TRP B 656 " --> pdb=" O HIS B 652 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 667 " --> pdb=" O TYR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 712 Processing helix chain 'B' and resid 716 through 748 Proline residue: B 742 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 100 removed outlier: 5.974A pdb=" N ARG A 51 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS A 95 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 53 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE A 97 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 55 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N HIS A 99 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A 57 " --> pdb=" O HIS A 99 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LYS A 122 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR A 54 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 124 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A 146 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 226 removed outlier: 6.513A pdb=" N ILE A 192 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE A 222 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 196 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE A 244 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 276 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 308 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A 420 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR A 435 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 422 " --> pdb=" O ILE A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 403 Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 468 Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 104 removed outlier: 5.833A pdb=" N LEU B 56 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG B 102 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE B 58 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR B 104 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY B 60 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N MET B 129 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N SER B 57 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N PHE B 131 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N MET B 59 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 225 through 232 removed outlier: 7.075A pdb=" N VAL B 198 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N GLU B 230 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR B 200 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE B 232 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR B 202 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG B 197 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N LEU B 252 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY B 199 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLN B 254 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 201 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TRP B 279 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL B 317 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 281 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N PHE B 319 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 426 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU B 441 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE B 428 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 410 Processing sheet with id=AA8, first strand: chain 'B' and resid 622 through 627 removed outlier: 3.553A pdb=" N ARG B 622 " --> pdb=" O GLU B 649 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1719 1.30 - 1.43: 2982 1.43 - 1.56: 6631 1.56 - 1.68: 58 1.68 - 1.81: 97 Bond restraints: 11487 Sorted by residual: bond pdb=" C38 U3D B 902 " pdb=" O37 U3D B 902 " ideal model delta sigma weight residual 1.330 1.449 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C20 U3D B 902 " pdb=" O22 U3D B 902 " ideal model delta sigma weight residual 1.330 1.431 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C40 U3D B 902 " pdb=" C41 U3D B 902 " ideal model delta sigma weight residual 1.527 1.615 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C24 U3G A 905 " pdb=" O23 U3G A 905 " ideal model delta sigma weight residual 1.337 1.424 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C18 U3G A 905 " pdb=" O20 U3G A 905 " ideal model delta sigma weight residual 1.334 1.419 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 11482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 15339 2.55 - 5.11: 252 5.11 - 7.66: 19 7.66 - 10.21: 2 10.21 - 12.77: 4 Bond angle restraints: 15616 Sorted by residual: angle pdb=" O28 U3D B 902 " pdb=" P27 U3D B 902 " pdb=" O29 U3D B 902 " ideal model delta sigma weight residual 122.96 110.19 12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C22 U3G A 905 " pdb=" O23 U3G A 905 " pdb=" C24 U3G A 905 " ideal model delta sigma weight residual 124.44 111.98 12.46 3.00e+00 1.11e-01 1.72e+01 angle pdb=" O46 U3G A 905 " pdb=" P47 U3G A 905 " pdb=" O50 U3G A 905 " ideal model delta sigma weight residual 97.04 109.31 -12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" O48 U3G A 905 " pdb=" P47 U3G A 905 " pdb=" O49 U3G A 905 " ideal model delta sigma weight residual 121.54 110.01 11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C GLN A 541 " pdb=" N PHE A 542 " pdb=" CA PHE A 542 " ideal model delta sigma weight residual 120.58 124.84 -4.26 1.32e+00 5.74e-01 1.04e+01 ... (remaining 15611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 6295 23.02 - 46.04: 359 46.04 - 69.06: 45 69.06 - 92.07: 10 92.07 - 115.09: 1 Dihedral angle restraints: 6710 sinusoidal: 2780 harmonic: 3930 Sorted by residual: dihedral pdb=" CA GLN B 432 " pdb=" C GLN B 432 " pdb=" N ASP B 433 " pdb=" CA ASP B 433 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PHE B 388 " pdb=" C PHE B 388 " pdb=" N ASN B 389 " pdb=" CA ASN B 389 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER B 434 " pdb=" C SER B 434 " pdb=" N ARG B 435 " pdb=" CA ARG B 435 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 6707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1555 0.063 - 0.127: 204 0.127 - 0.190: 15 0.190 - 0.254: 10 0.254 - 0.317: 8 Chirality restraints: 1792 Sorted by residual: chirality pdb=" C14 CLR A 906 " pdb=" C13 CLR A 906 " pdb=" C15 CLR A 906 " pdb=" C8 CLR A 906 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C14 CLR B 907 " pdb=" C13 CLR B 907 " pdb=" C15 CLR B 907 " pdb=" C8 CLR B 907 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C14 CLR B 906 " pdb=" C13 CLR B 906 " pdb=" C15 CLR B 906 " pdb=" C8 CLR B 906 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 1789 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 432 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C GLN B 432 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN B 432 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 433 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 695 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C VAL A 695 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A 695 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 696 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 696 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C ALA A 696 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 696 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 697 " 0.014 2.00e-02 2.50e+03 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 109 2.61 - 3.19: 10415 3.19 - 3.76: 16586 3.76 - 4.33: 23571 4.33 - 4.90: 38898 Nonbonded interactions: 89579 Sorted by model distance: nonbonded pdb=" OD2 ASP A 81 " pdb=" OH TYR A 354 " model vdw 2.042 3.040 nonbonded pdb=" OH TYR A 92 " pdb=" OE1 GLU A 379 " model vdw 2.113 3.040 nonbonded pdb=" O VAL B 364 " pdb=" OG1 THR B 368 " model vdw 2.115 3.040 nonbonded pdb=" OG SER A 508 " pdb=" OD1 ASP A 684 " model vdw 2.135 3.040 nonbonded pdb=" OE1 GLN B 87 " pdb=" OH TYR B 359 " model vdw 2.138 3.040 ... (remaining 89574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 11498 Z= 0.300 Angle : 0.797 12.766 15642 Z= 0.414 Chirality : 0.049 0.317 1792 Planarity : 0.004 0.046 1884 Dihedral : 14.099 115.092 4159 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.21), residues: 1338 helix: -0.58 (0.17), residues: 721 sheet: -1.84 (0.33), residues: 219 loop : -1.97 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.020 0.001 TYR A 535 PHE 0.018 0.001 PHE B 537 TRP 0.021 0.001 TRP B 676 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.30 (11487) covalent geometry : angle 0.78692 / 0.41 (15616) SS BOND : bond 0.00252 / 0.14 ( 7) SS BOND : angle 1.85093 / 0.84 ( 14) hydrogen bonds : bond 0.14535 / 10.02 ( 615) hydrogen bonds : angle 6.71732 / 4.76 ( 1803) link_NAG-ASN : bond 0.00544 / 0.27 ( 4) link_NAG-ASN : angle 4.36250 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 ASP cc_start: 0.7895 (t0) cc_final: 0.7235 (t0) REVERT: A 619 ARG cc_start: 0.7863 (ttt180) cc_final: 0.7620 (ttt180) REVERT: B 206 GLN cc_start: 0.7874 (tp40) cc_final: 0.7464 (tp-100) REVERT: B 272 MET cc_start: 0.7511 (mtp) cc_final: 0.7145 (mtp) REVERT: B 423 MET cc_start: 0.6209 (mmm) cc_final: 0.5990 (mmm) REVERT: B 734 ILE cc_start: 0.8561 (tt) cc_final: 0.8166 (tp) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1495 time to fit residues: 25.5086 Evaluate side-chains 96 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN A 170 HIS A 196 GLN A 236 ASN A 391 GLN A 513 ASN A 514 ASN A 685 HIS B 206 GLN B 278 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN B 506 ASN B 616 GLN B 647 HIS B 687 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.081507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.072921 restraints weight = 31627.927| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.14 r_work: 0.3212 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11498 Z= 0.138 Angle : 0.608 12.746 15642 Z= 0.307 Chirality : 0.043 0.207 1792 Planarity : 0.004 0.071 1884 Dihedral : 8.732 106.490 1620 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.36 % Allowed : 8.83 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.22), residues: 1338 helix: 0.96 (0.18), residues: 736 sheet: -1.41 (0.34), residues: 210 loop : -1.28 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 539 TYR 0.016 0.001 TYR A 535 PHE 0.017 0.001 PHE A 258 TRP 0.031 0.001 TRP B 676 HIS 0.003 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (11487) covalent geometry : angle 0.59315 / 0.30 (15616) SS BOND : bond 0.00216 / 0.15 ( 7) SS BOND : angle 1.01067 / 0.60 ( 14) hydrogen bonds : bond 0.04507 / 2.94 ( 615) hydrogen bonds : angle 4.66052 / 3.31 ( 1803) link_NAG-ASN : bond 0.00844 / 0.42 ( 4) link_NAG-ASN : angle 4.80681 / 2.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.8810 (mmm) cc_final: 0.8562 (mmt) REVERT: A 293 CYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6147 (p) REVERT: A 615 ASP cc_start: 0.8004 (t0) cc_final: 0.7753 (t0) REVERT: A 740 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8215 (tpp) REVERT: B 206 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8086 (tp-100) REVERT: B 272 MET cc_start: 0.7691 (mtp) cc_final: 0.7466 (mtp) REVERT: B 687 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8602 (t0) REVERT: B 734 ILE cc_start: 0.8894 (tt) cc_final: 0.8561 (tp) outliers start: 16 outliers final: 8 residues processed: 109 average time/residue: 0.1217 time to fit residues: 18.7303 Evaluate side-chains 101 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 687 ASN Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 53 optimal weight: 7.9990 chunk 112 optimal weight: 0.0570 chunk 95 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 97 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.081278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072725 restraints weight = 31909.751| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.14 r_work: 0.3210 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11498 Z= 0.136 Angle : 0.574 12.883 15642 Z= 0.288 Chirality : 0.042 0.219 1792 Planarity : 0.004 0.061 1884 Dihedral : 8.272 89.120 1620 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.04 % Allowed : 10.61 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1338 helix: 1.51 (0.19), residues: 738 sheet: -1.11 (0.34), residues: 207 loop : -1.08 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 89 TYR 0.020 0.001 TYR B 697 PHE 0.018 0.001 PHE A 222 TRP 0.031 0.001 TRP B 676 HIS 0.003 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11487) covalent geometry : angle 0.55832 / 0.28 (15616) SS BOND : bond 0.00200 / 0.12 ( 7) SS BOND : angle 1.05554 / 0.61 ( 14) hydrogen bonds : bond 0.04154 / 2.68 ( 615) hydrogen bonds : angle 4.41448 / 3.12 ( 1803) link_NAG-ASN : bond 0.00746 / 0.37 ( 4) link_NAG-ASN : angle 4.73308 / 2.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 615 ASP cc_start: 0.8025 (t0) cc_final: 0.7740 (t0) REVERT: A 630 LYS cc_start: 0.7175 (tptt) cc_final: 0.6943 (mmtt) REVERT: A 740 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8295 (tpp) REVERT: B 206 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8042 (tp-100) REVERT: B 272 MET cc_start: 0.7627 (mtp) cc_final: 0.7421 (mtp) REVERT: B 328 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7940 (mmmt) outliers start: 24 outliers final: 11 residues processed: 111 average time/residue: 0.1090 time to fit residues: 17.5600 Evaluate side-chains 102 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 71 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071534 restraints weight = 32115.664| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.15 r_work: 0.3182 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11498 Z= 0.182 Angle : 0.602 12.777 15642 Z= 0.303 Chirality : 0.043 0.220 1792 Planarity : 0.004 0.052 1884 Dihedral : 8.166 77.618 1619 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.29 % Allowed : 12.05 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1338 helix: 1.68 (0.19), residues: 736 sheet: -1.00 (0.35), residues: 209 loop : -1.04 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.020 0.002 TYR A 535 PHE 0.016 0.001 PHE A 258 TRP 0.034 0.001 TRP B 676 HIS 0.003 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (11487) covalent geometry : angle 0.58635 / 0.30 (15616) SS BOND : bond 0.00256 / 0.13 ( 7) SS BOND : angle 1.25641 / 0.71 ( 14) hydrogen bonds : bond 0.04322 / 2.79 ( 615) hydrogen bonds : angle 4.38657 / 3.10 ( 1803) link_NAG-ASN : bond 0.00773 / 0.39 ( 4) link_NAG-ASN : angle 4.73069 / 2.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7805 (mtt180) REVERT: A 615 ASP cc_start: 0.8066 (t0) cc_final: 0.7665 (t0) REVERT: A 630 LYS cc_start: 0.7202 (tptt) cc_final: 0.6894 (mmtt) REVERT: A 740 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8384 (tpp) REVERT: B 206 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8027 (tp-100) REVERT: B 272 MET cc_start: 0.7731 (mtp) cc_final: 0.7511 (mtp) REVERT: B 667 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8587 (mt) outliers start: 27 outliers final: 17 residues processed: 108 average time/residue: 0.1027 time to fit residues: 16.2605 Evaluate side-chains 111 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071634 restraints weight = 31729.161| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.14 r_work: 0.3185 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11498 Z= 0.168 Angle : 0.598 12.712 15642 Z= 0.298 Chirality : 0.042 0.222 1792 Planarity : 0.004 0.049 1884 Dihedral : 8.057 71.442 1619 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.78 % Allowed : 14.60 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1338 helix: 1.78 (0.19), residues: 735 sheet: -0.83 (0.35), residues: 208 loop : -1.05 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 539 TYR 0.019 0.001 TYR A 535 PHE 0.018 0.001 PHE A 222 TRP 0.036 0.001 TRP B 676 HIS 0.003 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (11487) covalent geometry : angle 0.58323 / 0.29 (15616) SS BOND : bond 0.00188 / 0.10 ( 7) SS BOND : angle 1.32256 / 0.73 ( 14) hydrogen bonds : bond 0.04189 / 2.68 ( 615) hydrogen bonds : angle 4.32626 / 3.06 ( 1803) link_NAG-ASN : bond 0.00773 / 0.39 ( 4) link_NAG-ASN : angle 4.64677 / 2.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 539 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.7919 (ttm-80) REVERT: A 615 ASP cc_start: 0.8063 (t0) cc_final: 0.7690 (t0) REVERT: A 630 LYS cc_start: 0.7220 (tptt) cc_final: 0.6909 (mmtt) REVERT: A 740 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8439 (tpp) REVERT: B 206 GLN cc_start: 0.8461 (tp-100) cc_final: 0.8037 (tp-100) REVERT: B 272 MET cc_start: 0.7661 (mtp) cc_final: 0.7454 (mtp) REVERT: B 328 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7942 (mttp) REVERT: B 711 PHE cc_start: 0.7467 (t80) cc_final: 0.7180 (m-10) outliers start: 21 outliers final: 16 residues processed: 106 average time/residue: 0.1044 time to fit residues: 16.2079 Evaluate side-chains 107 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 80 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN B 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.081293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072782 restraints weight = 31804.224| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.13 r_work: 0.3210 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11498 Z= 0.121 Angle : 0.551 12.544 15642 Z= 0.275 Chirality : 0.041 0.221 1792 Planarity : 0.004 0.049 1884 Dihedral : 7.817 67.011 1619 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.53 % Allowed : 15.45 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1338 helix: 2.00 (0.19), residues: 738 sheet: -0.63 (0.36), residues: 208 loop : -1.07 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 539 TYR 0.017 0.001 TYR B 697 PHE 0.016 0.001 PHE A 258 TRP 0.036 0.001 TRP B 676 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11487) covalent geometry : angle 0.53567 / 0.27 (15616) SS BOND : bond 0.00206 / 0.11 ( 7) SS BOND : angle 1.15926 / 0.63 ( 14) hydrogen bonds : bond 0.03804 / 2.43 ( 615) hydrogen bonds : angle 4.13145 / 2.90 ( 1803) link_NAG-ASN : bond 0.00798 / 0.40 ( 4) link_NAG-ASN : angle 4.51510 / 2.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 539 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.7899 (ttm-80) REVERT: A 615 ASP cc_start: 0.8047 (t0) cc_final: 0.7679 (t0) REVERT: A 630 LYS cc_start: 0.7134 (tptt) cc_final: 0.6846 (mmtt) REVERT: B 206 GLN cc_start: 0.8357 (tp-100) cc_final: 0.7924 (tp-100) REVERT: B 272 MET cc_start: 0.7574 (mtp) cc_final: 0.7346 (mtp) REVERT: B 328 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7756 (mmmt) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.0998 time to fit residues: 15.0959 Evaluate side-chains 104 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 72 optimal weight: 0.0040 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN B 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.082145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073765 restraints weight = 31614.677| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.07 r_work: 0.3236 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11498 Z= 0.106 Angle : 0.544 12.497 15642 Z= 0.269 Chirality : 0.040 0.219 1792 Planarity : 0.003 0.049 1884 Dihedral : 7.594 62.483 1619 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.53 % Allowed : 15.45 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1338 helix: 2.19 (0.19), residues: 736 sheet: -0.50 (0.36), residues: 206 loop : -1.00 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 539 TYR 0.016 0.001 TYR B 697 PHE 0.017 0.001 PHE A 222 TRP 0.036 0.001 TRP B 676 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (11487) covalent geometry : angle 0.52898 / 0.27 (15616) SS BOND : bond 0.00220 / 0.13 ( 7) SS BOND : angle 1.13485 / 0.61 ( 14) hydrogen bonds : bond 0.03580 / 2.29 ( 615) hydrogen bonds : angle 4.06059 / 2.84 ( 1803) link_NAG-ASN : bond 0.00808 / 0.40 ( 4) link_NAG-ASN : angle 4.45656 / 2.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 539 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.7895 (ttm-80) REVERT: A 615 ASP cc_start: 0.8021 (t0) cc_final: 0.7633 (t0) REVERT: A 630 LYS cc_start: 0.7101 (tptt) cc_final: 0.6846 (mmtt) REVERT: B 206 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7854 (tp-100) REVERT: B 272 MET cc_start: 0.7500 (mtp) cc_final: 0.7260 (mtp) REVERT: B 328 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7850 (mmmt) REVERT: B 631 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5769 (pm20) outliers start: 18 outliers final: 15 residues processed: 105 average time/residue: 0.1049 time to fit residues: 16.3183 Evaluate side-chains 103 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 134 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.073357 restraints weight = 31685.651| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.13 r_work: 0.3225 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11498 Z= 0.119 Angle : 0.555 12.537 15642 Z= 0.276 Chirality : 0.041 0.222 1792 Planarity : 0.004 0.047 1884 Dihedral : 7.571 58.092 1619 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.78 % Allowed : 15.53 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1338 helix: 2.18 (0.19), residues: 739 sheet: -0.46 (0.36), residues: 206 loop : -0.95 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 539 TYR 0.015 0.001 TYR B 697 PHE 0.016 0.001 PHE A 544 TRP 0.040 0.001 TRP B 676 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11487) covalent geometry : angle 0.54066 / 0.27 (15616) SS BOND : bond 0.00211 / 0.12 ( 7) SS BOND : angle 1.12761 / 0.61 ( 14) hydrogen bonds : bond 0.03631 / 2.32 ( 615) hydrogen bonds : angle 4.05707 / 2.83 ( 1803) link_NAG-ASN : bond 0.00809 / 0.41 ( 4) link_NAG-ASN : angle 4.47318 / 2.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 ASP cc_start: 0.8090 (t0) cc_final: 0.7740 (t0) REVERT: A 630 LYS cc_start: 0.7087 (tptt) cc_final: 0.6804 (mmtt) REVERT: B 206 GLN cc_start: 0.8293 (tp-100) cc_final: 0.7842 (tp-100) REVERT: B 272 MET cc_start: 0.7550 (mtp) cc_final: 0.7313 (mtp) REVERT: B 328 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7862 (mttp) REVERT: B 631 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5757 (pm20) outliers start: 21 outliers final: 18 residues processed: 107 average time/residue: 0.1027 time to fit residues: 16.1759 Evaluate side-chains 109 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 30 optimal weight: 0.0170 overall best weight: 1.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072970 restraints weight = 31652.402| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.12 r_work: 0.3215 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11498 Z= 0.134 Angle : 0.566 12.587 15642 Z= 0.281 Chirality : 0.041 0.224 1792 Planarity : 0.004 0.047 1884 Dihedral : 7.609 58.723 1619 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.95 % Allowed : 15.70 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1338 helix: 2.18 (0.19), residues: 739 sheet: -0.46 (0.36), residues: 206 loop : -0.89 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 539 TYR 0.015 0.001 TYR A 535 PHE 0.022 0.001 PHE A 544 TRP 0.043 0.001 TRP B 676 HIS 0.002 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11487) covalent geometry : angle 0.55174 / 0.28 (15616) SS BOND : bond 0.00234 / 0.12 ( 7) SS BOND : angle 1.13801 / 0.62 ( 14) hydrogen bonds : bond 0.03704 / 2.37 ( 615) hydrogen bonds : angle 4.06883 / 2.84 ( 1803) link_NAG-ASN : bond 0.00804 / 0.40 ( 4) link_NAG-ASN : angle 4.49879 / 2.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 ASP cc_start: 0.8103 (t0) cc_final: 0.7764 (t0) REVERT: A 630 LYS cc_start: 0.7114 (tptt) cc_final: 0.6859 (mmtt) REVERT: B 206 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7859 (tp-100) REVERT: B 272 MET cc_start: 0.7583 (mtp) cc_final: 0.7363 (mtp) REVERT: B 328 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7825 (mmmt) REVERT: B 631 GLU cc_start: 0.5991 (OUTLIER) cc_final: 0.5784 (pm20) outliers start: 23 outliers final: 19 residues processed: 109 average time/residue: 0.1065 time to fit residues: 17.1464 Evaluate side-chains 112 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 730 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 101 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.081766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.073318 restraints weight = 31725.487| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.13 r_work: 0.3224 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11498 Z= 0.119 Angle : 0.558 12.481 15642 Z= 0.278 Chirality : 0.041 0.224 1792 Planarity : 0.004 0.047 1884 Dihedral : 7.490 55.386 1619 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 1.70 % Allowed : 16.30 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1338 helix: 2.23 (0.19), residues: 738 sheet: -0.43 (0.36), residues: 206 loop : -0.83 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 539 TYR 0.015 0.001 TYR B 697 PHE 0.013 0.001 PHE A 258 TRP 0.046 0.001 TRP B 676 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11487) covalent geometry : angle 0.54340 / 0.27 (15616) SS BOND : bond 0.00224 / 0.12 ( 7) SS BOND : angle 1.08619 / 0.59 ( 14) hydrogen bonds : bond 0.03608 / 2.31 ( 615) hydrogen bonds : angle 4.03453 / 2.82 ( 1803) link_NAG-ASN : bond 0.00815 / 0.41 ( 4) link_NAG-ASN : angle 4.45020 / 2.62 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 ASP cc_start: 0.8099 (t0) cc_final: 0.7760 (t0) REVERT: A 630 LYS cc_start: 0.7065 (tptt) cc_final: 0.6764 (mmtt) REVERT: B 206 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7821 (tp-100) REVERT: B 272 MET cc_start: 0.7512 (mtp) cc_final: 0.7295 (mtp) REVERT: B 328 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7820 (mmmt) REVERT: B 631 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5902 (pm20) outliers start: 20 outliers final: 18 residues processed: 108 average time/residue: 0.1056 time to fit residues: 16.9353 Evaluate side-chains 109 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 535 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 111 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.081678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.073144 restraints weight = 31854.906| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.14 r_work: 0.3218 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11498 Z= 0.124 Angle : 0.563 12.476 15642 Z= 0.279 Chirality : 0.041 0.223 1792 Planarity : 0.004 0.047 1884 Dihedral : 7.483 56.243 1619 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.04 % Allowed : 16.04 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1338 helix: 2.22 (0.19), residues: 739 sheet: -0.41 (0.37), residues: 206 loop : -0.83 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 539 TYR 0.015 0.001 TYR B 697 PHE 0.012 0.001 PHE A 222 TRP 0.046 0.001 TRP B 676 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (11487) covalent geometry : angle 0.54874 / 0.28 (15616) SS BOND : bond 0.00222 / 0.12 ( 7) SS BOND : angle 1.09875 / 0.60 ( 14) hydrogen bonds : bond 0.03626 / 2.33 ( 615) hydrogen bonds : angle 4.04986 / 2.83 ( 1803) link_NAG-ASN : bond 0.00811 / 0.41 ( 4) link_NAG-ASN : angle 4.45861 / 2.62 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2639.89 seconds wall clock time: 46 minutes 21.69 seconds (2781.69 seconds total)